Name

recons3d_4nn_ctf - calculate CTF-corrected 3-D reconstruction from a set of projections using three Eulerian angles, two shifts, and CTF settings for each projeciton image

Usage

# calculate reconstruction using odd-numbered projections

• stack = "my_data.hdf"
• numproj = EMUtil.get_image_count(stack)
• list_proj = range(0,numproj,2):
• vol = recons3d_4nn_ctf(stack, list_proj, snr, sign [, symmetry])

Input

stack

name of the stack file containing projection data, projections have to be squares, i.e., nx=ny

list_proj

list of projections to be included in the reconstruction

snr

Signal-to-Noise Ratio of the data (default = 1.0)

sign

sign of the CTF (for convenience for cry data the sign of the CTF is usually inverted and set to +1 so the particles appear to be bright on the dark background) (default = 1)

symmetry

point-group symmetry to be enforced, each projection will enter the reconstruction in all symmetry-related directions. The possibilities are

"cn"

"dn"

"i"

default is "c1" (no symmetry).

Output

vol

the 3-D reconstructed volume

Description

The command requires all parameters to be stored in headers of projection images as:

• proj.set_attr_dict({'phi':phi, 'theta':theta, 'psi':psi, 's2x':sx, 's2y':sy})
• proj.set_attr_dict({'ctf_applied':0})

• CTF parameters need to be stored as an EMAN CTF object (see CTF_info for more information)

If projection images were already multiplied by the CTF, set attribute ctf_applied to 1.

Method

Reference

Author / Maintainer

Pawel A. Penczek

Keywords

category 1

INVERSION

category 2

FOURIER

Files

reconstruction.py

See also

recons3d_4nn, recons3d_sirt

Bugs

None. It is perfect.